Tamarillo extract is a good source of phenolic and anthocyanin compounds which are well-known for beneficial antioxidant activity, but their bioactivity maybe lost during digestion. In this study, promising prospects of tamarillo polyphenols encapsulated in cubosome nanoparticles prepared via a top-down method were explored. The prepared nanocarriers were examined for their morphology, entrapment efficiency, particle size and stability during in vitro digestion as well as potential fortification of yoghurt. Tamarillo polyphenol-loaded cubosomes showed cubic shape with a mean particle size of 322.4 ± 7.27 nm and the entrapment efficiency for most polyphenols was over 50%. The encapsulated polyphenols showed high stability during the gastric phase of in vitro digestion and were almost completely, but slowly released in the intestinal phase. Addition of encapsulated tamarillo polyphenols to yoghurt (5, 10 and 15 wt% through pre- and post-fermentation) improved the physicochemical and potential nutritional properties (polyphenols concentration, TPC) as well as antioxidant activity. The encapsulation of tamarillo polyphenols protected against pH changes and enzymatic digestion and facilitated a targeted delivery and slow release of the encapsulated compounds to the intestine. Overall, the cubosomal delivery system demonstrated the potential for encapsulation of polyphenols from tamarillo for value-added food product development with yoghurt as the vehicle.